The ability to separate, quantify, and determine structure of trace levels of Class II antigenic peptides allow research to be expedited in fundamental immunology. We are exploring immuno-affinity coupled with reverse-phase HPLC, micro HPLC, nano HPLC and ion exchange coupled with micro HPLC to separate antigenic peptides from other closely related peptides. Identification will be either by matrix-assisted laser desorption ionization, monitoring post-source decomposition's, or by HPLC and the ion trap using electrospray or nano-electrospray (Finnigan LCQ). We also seek to develop methods for quantification of complex peptide mixtures by MALDI.